Try to fix Read the Docs

.readthedocs.yaml

@@ -1,16 +1,28 @@
-version:  2
+version: 2
 
 build:
-  os:  ubuntu-22.04
+  os: ubuntu-lts-latest
   tools:
-    python:  "3.10"
+    python: "mambaforge-latest"
+  jobs:
+    post_checkout:
+      - git fetch --unshallow || true
+    pre_install:
+      - git update-index --assume-unchanged .rtd-environment.yml docs/source/conf.py
+
+conda:
+  environment: .rtd-environment.yml
 
 sphinx:
-  configuration:  docs/source/conf.py
+  builder: html
+  configuration: docs/source/conf.py
+  fail_on_warning: false
+
+formats:
+  - htmlzip
 
 # Optionally declare the Python requirements required to build your docs
 python:
    install:
-   - requirements: docs/requirements.txt
-   - method: pip
-     path: .
+   - requirements: requirements.txt
+   - method: setuptools

.rtd-environment.yml

@@ -0,0 +1,7 @@
+name: rtd_chiantipy
+channels:
+  - conda-forge
+dependencies:
+  - python=3.12
+  - pip
+  - graphviz!=2.42.*,!=2.43.*

ChiantiPy/base/_IonTrails.py

@@ -78,7 +78,7 @@ def argCheck(self, temperature=None, eDensity=None, pDensity='default', em = Non
 
     def intensityList(self, index=None, wvlRange=None, wvlRanges=None, top=10, integrated=False,
         relative=0, outFile=0, rightDigits=4):
-        """
+        r"""
         List the line intensities. Checks to see if there is an existing Intensity attribute.
         If it exists, then those values are used.
         Otherwise, the `intensity` method is called.
@@ -104,30 +104,28 @@ def intensityList(self, index=None, wvlRange=None, wvlRanges=None, top=10, integ
         to 'energy', the intensity is given by,
 
         .. math::
-           I = \\Delta E_{ij}n_jA_{ij}\\mathrm{Ab}\\frac{1}{N_e}
-           \\frac{N(X^{+m})}{N(X)}\\mathrm{EM},
+           I = \Delta E_{ij}n_jA_{ij}\mathrm{Ab}\frac{1}{N_e}\frac{N(X^{+m})}{N(X)}\mathrm{EM},
 
-        in units of ergs cm\\ :sup:`-2` s\\ :sup:`-1` sr \\ :sup:`-1`. If 'flux' is set to 'photon',
+        in units of ergs cm\ :sup:`-2` s\ :sup:`-1` sr \ :sup:`-1`. If 'flux' is set to 'photon',
 
         .. math::
-           I = n_jA_{ij}\\mathrm{Ab}\\frac{1}{N_e}\\frac{N(X^{+m})}{N(X)}
-           \\mathrm{EM},
+           I = n_jA_{ij}\mathrm{Ab}\frac{1}{N_e}\frac{N(X^{+m})}{N(X)}\mathrm{EM},
 
         where,
 
-        - :math:`\\Delta E_{ij}` is the transition energy (ergs)
+        - :math:`\Delta E_{ij}` is the transition energy (ergs)
         - :math:`n_j` is  the fractions of ions in level :math:`j`
         - :math:`A_{ij}` is the Einstein coefficient for spontaneous emission
-          from level :math:`j` to level :math:`i` (in s\\ :sup:`-1`)
-        - :math:`\\mathrm{Ab}` is the abundance of the specified element
+          from level :math:`j` to level :math:`i` (in s\ :sup:`-1`)
+        - :math:`\mathrm{Ab}` is the abundance of the specified element
           relative to hydrogen
-        - :math:`N_e` is the electron density (in cm\\ :sup:`-3`)
+        - :math:`N_e` is the electron density (in cm\ :sup:`-3`)
         - :math:`N(X^{+m})/N(X)` is the fractional ionization of ion as a
           function of temperature
-        - :math:`\\mathrm{EM}` is the emission measure integrated along the
-          line-of-sight, :math:`\\int\\mathrm{d}l\\,N_eN_H` (cm\\ :sup:`-5`) where
+        - :math:`\mathrm{EM}` is the emission measure integrated along the
+          line-of-sight, :math:`\int\mathrm{d}l\,N_eN_H` (cm\ :sup:`-5`) where
           :math:`N_H` is the density of hydrogen (neutral + ionized)
-          (cm\\ :sup:`-3`)
+          (cm\ :sup:`-3`)
 
         Note that if `relative` is set, the line intensity is relative to the
         strongest line and so the output will be unitless.

ChiantiPy/core/Bunch.py

@@ -13,7 +13,7 @@
 
 
 class bunch(ionTrails, specTrails):
-    '''
+    r'''
     Calculate the emission line spectrum as a function of temperature and density.
 
     'bunch' is very similar to 'spectrum' except that continuum is not calculated and
@@ -67,7 +67,7 @@ class instance of ChiantiPy.core.ion for 'mg_7'.  All its methods and attributes
         the temperature(s) in K
 
     eDensity: float, ndarray
-        eDensity: electron density in :math:`\\mathrm{cm^{-3}}`
+        eDensity: electron density in :math:`\mathrm{cm^{-3}}`
 
     wvlRange:  2 element `list` or `ndarray`
         wvlRange:  range of wavelengths to consider, generally in angstroms

ChiantiPy/core/Continuum.py

@@ -21,7 +21,7 @@
 
 
 class continuum(ionTrails):
-    """
+    r"""
     The top level class for continuum calculations. Includes methods for the calculation of the
     free-free and free-bound continua.
 
@@ -38,9 +38,9 @@ class continuum(ionTrails):
         Elemental abundance relative to Hydrogen or name of CHIANTI abundance file,
         without the '.abund' suffix, e.g. 'sun_photospheric_1998_grevesse'.
     em : array-like, optional
-        Line-of-sight emission measure (:math:`\\int\\mathrm{d}l\\,n_en_H`), in units of
-        :math:`\\mathrm{cm}^{-5}`, or the volumetric emission measure (:math:`\\int\\mathrm{d}V\\,n_en_H`)
-        in units of :math:`\\mathrm{cm}^{-3}`.
+        Line-of-sight emission measure (:math:`\int\mathrm{d}l\,n_en_H`), in units of
+        :math:`\mathrm{cm}^{-5}`, or the volumetric emission measure (:math:`\int\mathrm{d}V\,n_en_H`)
+        in units of :math:`\mathrm{cm}^{-3}`.
     verbose : `bool`
         if True, prints additional info to the console
 
@@ -123,21 +123,21 @@ def __init__(self, ionStr,  temperature, abundance=None, em=None, verbose=0):
         self.ioneqOne()
 
     def free_free_loss(self,  includeAbund=True, includeIoneq=True, **kwargs):
-        """
+        r"""
         Calculate the free-free energy loss rate of an ion. The result is returned to the
         `free_free_loss` attribute.
 
         The free-free radiative loss rate is given by Eq. 5.15a of [107]_. Writing the numerical
-        constant in terms of the fine structure constant :math:`\\alpha`,
+        constant in terms of the fine structure constant :math:`\alpha`,
 
         .. math::
-           \\frac{dW}{dtdV} = \\frac{4\\alpha^3h^2}{3\\pi^2m_e}\\left(\\frac{2\\pi k_B}{3m_e}\\right)^{1/2}Z^2T^{1/2}\\bar{g}_B
+           \frac{dW}{dtdV} = \frac{4\alpha^3h^2}{3\pi^2m_e}\left(\frac{2\pi k_B}{3m_e}\right)^{1/2}Z^2T^{1/2}\bar{g}_B
 
         where where :math:`Z` is the nuclear charge, :math:`T` is the electron temperature, and
         :math:`\\bar{g}_{B}` is the wavelength-averaged and velocity-averaged Gaunt factor. The
         Gaunt factor is calculated using the methods of [103]_. Note that this expression for the
         loss rate is just the integral over wavelength of Eq. 5.14a of [107]_, the free-free emission, and
-        is expressed in units of erg :math:`\\mathrm{cm}^3\\,\\mathrm{s}^{-1}`.
+        is expressed in units of erg :math:`\mathrm{cm}^3\,\mathrm{s}^{-1}`.
 
         """
         # interpolate wavelength-averaged K&L gaunt factors
@@ -159,7 +159,7 @@ def free_free_loss(self,  includeAbund=True, includeIoneq=True, **kwargs):
         self.FreeFreeLoss = prefactor*(self.Zion**2)*np.sqrt(self.Temperature)*gaunt_factor
 
     def freeFree(self, wavelength, includeAbund=True, includeIoneq=True, **kwargs):
-        """
+        r"""
         Calculates the free-free emission for a single ion. The result is returned as a dict to
         the `FreeFree` attribute.  The dict has the keywords `intensity`, `wvl`, `temperature`, `em`.
 
@@ -168,17 +168,17 @@ def freeFree(self, wavelength, includeAbund=True, includeIoneq=True, **kwargs):
         constant in terms of the fine structure constant :math:`\\alpha`,
 
         .. math::
-           \\frac{dW}{dtdVd\\lambda} = \\frac{c}{3m_e}\\left(\\frac{\\alpha h}{\\pi}\\right)^3\\left(\\frac{2\\pi}{3m_ek_B}\\right)^{1/2}\\frac{Z^2}{\\lambda^2T^{1/2}}\\exp{\\left(-\\frac{hc}{\\lambda k_BT}\\right)}\\bar{g}_{ff},
+           \frac{dW}{dtdVd\\lambda} = \frac{c}{3m_e}\left(\frac{\alpha h}{\pi}\right)^3\left(\frac{2\pi}{3m_ek_B}\right)^{1/2}\frac{Z^2}{\lambda^2T^{1/2}}\exp{\left(-\frac{hc}{\lambda k_BT}\right)}\bar{g}_{ff},
 
         where :math:`Z` is the nuclear charge, :math:`T` is the electron temperature in K, and
-        :math:`\\bar{g}_{ff}` is the velocity-averaged Gaunt factor. The Gaunt factor is estimated
+        :math:`\bar{g}_{ff}` is the velocity-averaged Gaunt factor. The Gaunt factor is estimated
         using the methods of [104]_ and [101]_, depending on the temperature and energy regime. See
         `itoh_gaunt_factor` and `sutherland_gaunt_factor` for more details.
 
         The free-free emission is in units of erg
-        :math:`\\mathrm{cm}^3\\mathrm{s}^{-1}\\mathrm{\\mathring{A}}^{-1}\\mathrm{str}^{-1}`. If the emission
-        measure has been set, the units will be multiplied by :math:`\\mathrm{cm}^{-5}` or
-        :math:`\\mathrm{cm}^{-3}`, depending on whether it is the line-of-sight or volumetric
+        :math:`\mathrm{cm}^3\mathrm{s}^{-1}\mathrm{\mathring{A}}^{-1}\mathrm{str}^{-1}`. If the emission
+        measure has been set, the units will be multiplied by :math:`\mathrm{cm}^{-5}` or
+        :math:`\mathrm{cm}^{-3}`, depending on whether it is the line-of-sight or volumetric
         emission measure, respectively.
 
         Parameters

ChiantiPy/core/Ion.py

@@ -26,7 +26,7 @@
 
 
 class ion(ioneqOne, ionTrails, specTrails):
-    """
+    r"""
     The top level class for performing spectral calculations for an ion in the
     CHIANTI database.
 
@@ -37,9 +37,9 @@ class ion(ioneqOne, ionTrails, specTrails):
     temperature : `float` , `tuple`, `list`, `~numpy.ndarray`, optional
         Temperature array (Kelvin)
     eDensity : `float` , `tuple`, `list`, or `~numpy.ndarray`, optional
-        Electron density array (:math:r`\\mathrm{cm^{-3}}` )
+        Electron density array (:math:`\mathrm{cm^{-3}}` )
     pDensity : `float`, `tuple`, `list` or `~numpy.ndarray`, optional
-        Proton density (:math:r`\\mathrm{cm}^{-3}` )
+        Proton density (:math:`\mathrm{cm}^{-3}` )
     radTemperature : `float` or `~numpy.ndarray`, optional
         Radiation black-body temperature (in Kelvin)
     rStar : `float` or `~numpy.ndarray`, optional
@@ -52,9 +52,9 @@ class ion(ioneqOne, ionTrails, specTrails):
         attributes of the selected ion
     em : `float` or `~numpy.ndarray`, optional
         Emission Measure, for the line-of-sight emission measure
-        (:math:r`\\mathrm{\\int \\, n_e \\, n_H \\, dl}`)
-        (:math:r`\\mathrm{cm}^{-5}`.), for the volumetric emission measure
-        :math:r`\\mathrm{\\int \\, n_e \\, n_H \\, dV}` (:math:r`\\mathrm{cm^{-3}}`).
+        (:math:`\mathrm{\int \, n_e \, n_H \, dl}`)
+        (:math:`\mathrm{cm}^{-5}`.), for the volumetric emission measure
+        :math:`\mathrm{\int \, n_e \, n_H \, dV}` (:math:`\mathrm{cm^{-3}}`).
 
     Attributes
     ----------

ChiantiPy/core/Ioneq.py

@@ -14,26 +14,23 @@
 from .Ion import ion
 
 def ioneqMake(filename, directory = None, temperature = None,  reference = None, verbose = False):
-    """a function  to create a chianit .ioneq style ionization equilibrium
+    """
+    A function to create a chianti .ioneq style ionization equilibrium
+
     Parameters
     ----------
-
     filename:  `str`
         the name of the file to be created - should end in .ioneq
-
     directory: `str`
         the directory where the file will be placed.  If it is None, the the file
         will be placed in the uses home directory.
-
     temperature:  `array-like`
         the temperatures at which the ionization equilibrium will be calculated
         the default value is None and the temperature will be 101 values exponentially
         spaced between 10^4 and 10^9 K
-
     reference:  `list` of `str`
         a list of references to be added to tail of file.
         such as ['file created by me', 'today']
-
     verbose:  `bool`
         if True, prints out information, the default is False
     """

ChiantiPy/core/IpyMspectrum.py

@@ -101,7 +101,7 @@ def __init__(self, temperature, eDensity, wavelength, filter=(chfilters.gaussian
         ylabel = self.Labels['spectrumYlabel']
 
         if np.array_equal(self.Em, np.ones_like(self.Em)):
-            ylabel += '($\int\,$ N$_e\,$N$_H\,$d${\it l}$)$^{-1}$'
+            ylabel += r'($\int\,$ N$_e\,$N$_H\,$d${\it l}$)$^{-1}$'
         #
         self.AllLines = allLines
         #

ChiantiPy/core/MradLoss.py

@@ -16,70 +16,47 @@
 
 
 class mradLoss(ionTrails, specTrails):
-    """    Calculate the radiative emission loss rate as a function of temperature and density.
+    r"""
+    Calculate the radiative emission loss rate as a function of temperature and density.
 
-    this is the multiprocessing version of radloss
+    This is the multiprocessing version of radloss. It includes elemental abundances or
+    ionization equilibria. Temperature and density can be arrays but, unless the size of
+    either is one (1), the two must have the same size
 
-    includes elemental abundances or ionization equilibria
-
-    temperature and density can be arrays but, unless the size of either is one (1),
-    the two must have the same size
-
-
-    A selection of ions can be make with ionList containing the names of
-    the desired lines in Chianti notation,
-    i.e. C VI = c_6
-
-    a minimum abundance can be specified so that the calculation can be speeded up by excluding
+    A minimum abundance can be specified so that the calculation can be speeded up by excluding
     elements with a low abundance. With solar photospheric abundances
 
-    setting minAbund = 1.e-4 will include H, He, C, O, Ne
-    setting minAbund = 2.e-5 adds  N, Mg, Si, S, Fe
-    setting minAbund = 1.e-6 adds  Na, Al, Ar, Ca, Ni
-
-    Setting em will multiply the spectrum at each temperature by the value of em.
-
-    em (for emission measure), can be a float or an array of the same length as the
-    temperature/density.
-
-    abundance: to select a particular set of abundances, set abundance to the name of a
-        CHIANTI abundance file, without the '.abund' suffix, e.g. 'sun_photospheric_1998_grevesse'
-        If set to a blank (''), a gui selection menu will popup and allow the
-        selection of an set of abundances
+    - setting minAbund = 1.e-4 will include H, He, C, O, Ne
+    - setting minAbund = 2.e-5 adds  N, Mg, Si, S, Fe
+    - setting minAbund = 1.e-6 adds  Na, Al, Ar, Ca, Ni
 
     Parameters
     --------------
-
     temperature: `float`, `list`, `ndarray`
         the temperature(s) in K
-
     eDensity: float, ndarray
-        eDensity: electron density in :math:`\mathrm{cm^{-3}}`
-
+        electron density in :math:`\mathrm{cm^{-3}}`
     elementList:  `list`
-        elementList:  list of elements to include, such as 'fe', 'ne', 's'
-
+        list of elements to include, such as 'fe', 'ne', 's'
     ionList:  `list`
-        ionList:  list of ions to include, such as 'fe_16', 'ne_10'
-
+        list of ions to include, such as 'fe_16', 'ne_10'
     minAbund:  `float`
-        minAbund:  minimum abundance (relative to H) to include
-
-    doLines:  `bool1
-        doLines: if true, line intensities are calculated
-
+        minimum abundance (relative to H) to include
+    doLines:  `bool`
+        if true, line intensities are calculated
     doContinuum:  `bool`
-        doContinuum:  if true, continuum intensities are calculated only if wavelengths are in angstroms
-
+        if true, continuum intensities are calculated only if wavelengths are in angstroms
     abundance:  `str`
-        abuncance:  the file name of the abuncance set to be used
-            must be one in the $XUVTOP/abund directory
-
+        the file name of the abuncance set to be used
+        must be one in the $XUVTOP/abund directory
+        to select a particular set of abundances, set abundance to the name of a
+        CHIANTI abundance file, without the '.abund' suffix, e.g. 'sun_photospheric_1998_grevesse'
+        If set to a blank (''), a gui selection menu will popup and allow the
+        selection of an set of abundances
     allLInes:  `bool`
-        allLines:  whether or not to include unobserved lines
-
+        whether or not to include unobserved lines
     verbose:  `bool`
-        verbose:  whether to allow certain print statements
+        whether to allow certain print statements
 
     """
     def __init__(self, temperature, eDensity, elementList=None, ionList = None, minAbund=None,